Revision 22abd4ac
Added by Andreas Müller over 7 years ago
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java | ||
|---|---|---|
| 615 | 615 |
this.relationsFromThisTaxon.remove(rel); |
| 616 | 616 |
Taxon fromTaxon = rel.getFromTaxon(); |
| 617 | 617 |
Taxon toTaxon = rel.getToTaxon(); |
| 618 |
// check if this removes the taxonomical parent. If so, also remove shortcut to the higher taxon |
|
| 619 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) ){
|
|
| 620 |
if (fromTaxon != null && fromTaxon.equals(this)){
|
|
| 621 |
this.taxonomicParentCache = null; |
|
| 622 |
}else if (toTaxon != null && toTaxon.equals(this)){
|
|
| 623 |
this.setTaxonomicChildrenCount(computeTaxonomicChildrenCount()); |
|
| 624 |
} |
|
| 625 |
} |
|
| 618 |
|
|
| 626 | 619 |
//delete Relationship from other related Taxon |
| 627 | 620 |
if (fromTaxon != this){
|
| 628 | 621 |
rel.setToTaxon(null); //remove this Taxon from relationship |
| ... | ... | |
| 672 | 665 |
if (toTaxon!=null){
|
| 673 | 666 |
toTaxon.addTaxonRelation(rel); |
| 674 | 667 |
} |
| 675 |
// check if this sets the taxonomical parent. If so, remember a shortcut to this taxon |
|
| 676 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && toTaxon!=null ){
|
|
| 677 |
this.taxonomicParentCache = toTaxon; |
|
| 678 |
} |
|
| 679 | 668 |
}else if (this.equals(toTaxon)){
|
| 680 | 669 |
relationsToThisTaxon.add(rel); |
| 681 | 670 |
// also add relation to other taxon object |
| 682 | 671 |
if (fromTaxon!=null){
|
| 683 | 672 |
fromTaxon.addTaxonRelation(rel); |
| 684 | 673 |
} |
| 685 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && fromTaxon!=null ){
|
|
| 686 |
this.taxonomicChildrenCount++; |
|
| 687 |
} |
|
| 688 |
|
|
| 689 | 674 |
} |
| 690 | 675 |
}else if (toTaxon == null || fromTaxon == null){
|
| 691 | 676 |
if (toTaxon == null){
|
| ... | ... | |
| 694 | 679 |
if (fromTaxon!= null){
|
| 695 | 680 |
fromTaxon.addTaxonRelation(rel); |
| 696 | 681 |
} |
| 697 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && fromTaxon!=null ){
|
|
| 698 |
this.taxonomicChildrenCount++; |
|
| 699 |
} |
|
| 700 | 682 |
}else if (fromTaxon == null && toTaxon != null){
|
| 701 | 683 |
fromTaxon = this; |
| 702 | 684 |
relationsFromThisTaxon.add(rel); |
| 703 |
if (toTaxon!=null){
|
|
| 704 |
toTaxon.addTaxonRelation(rel); |
|
| 705 |
} |
|
| 706 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && toTaxon!=null ){
|
|
| 707 |
this.taxonomicParentCache = toTaxon; |
|
| 708 |
} |
|
| 685 |
toTaxon.addTaxonRelation(rel); |
|
| 709 | 686 |
} |
| 710 | 687 |
} |
| 711 | 688 |
} |
| 712 | 689 |
} |
| 713 | 690 |
|
| 714 |
/* (non-Javadoc) |
|
| 715 |
* @see eu.etaxonomy.cdm.model.common.IRelated#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase) |
|
| 716 |
*/ |
|
| 691 |
|
|
| 717 | 692 |
@Override |
| 718 | 693 |
@Deprecated //for inner use by RelationshipBase only |
| 719 | 694 |
public void addRelationship(RelationshipBase rel){
|
| ... | ... | |
| 806 | 781 |
} |
| 807 | 782 |
} |
| 808 | 783 |
|
| 809 |
/** |
|
| 810 |
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
|
| 811 |
* "taxonomically included in") instance where <i>this</i> taxon plays the target |
|
| 812 |
* role (parent) and adds it to the set of |
|
| 813 |
* {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging to <i>this</i> taxon.
|
|
| 814 |
* The taxon relationship will also be added to the set of |
|
| 815 |
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the second taxon
|
|
| 816 |
* (child) involved in the created relationship.<P> |
|
| 817 |
* Since the taxon relationship concerns the modifications |
|
| 818 |
* of the number of {@link #getTaxonomicChildrenCount() childrens} for <i>this</i> taxon and
|
|
| 819 |
* of the {@link #getTaxonomicParent() parent taxon} for the child taxon will be stored.
|
|
| 820 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 821 |
* than the rank of the taxon name used as a child taxon. |
|
| 822 |
* |
|
| 823 |
* @param child the taxon which plays the source role (child) in the new taxon relationship |
|
| 824 |
* @param citation the reference source for the new taxon relationship |
|
| 825 |
* @param microcitation the string with the details describing the exact localisation within the reference |
|
| 826 |
* @see #setTaxonomicParent(Taxon, Reference, String) |
|
| 827 |
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String) |
|
| 828 |
* @see #addTaxonRelation(TaxonRelationship) |
|
| 829 |
* @see #getTaxonRelations() |
|
| 830 |
* @see #getRelationsFromThisTaxon() |
|
| 831 |
* @see #getRelationsToThisTaxon() |
|
| 832 |
* @see #getTaxonomicParent() |
|
| 833 |
* @see #getTaxonomicChildrenCount() |
|
| 834 |
*/ |
|
| 835 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 836 |
public void addTaxonomicChild(Taxon child, Reference citation, String microcitation){
|
|
| 837 |
if (child == null){
|
|
| 838 |
throw new NullPointerException("Child Taxon is 'null'");
|
|
| 839 |
}else{
|
|
| 840 |
child.setTaxonomicParent(this, citation, microcitation); |
|
| 841 |
} |
|
| 842 |
} |
|
| 843 |
|
|
| 844 |
/** |
|
| 845 |
* Removes one {@link TaxonRelationship taxon relationship} with {@link TaxonRelationshipType taxon relationship type}
|
|
| 846 |
* "taxonomically included in" and with the given child taxon playing the |
|
| 847 |
* source role from the set of {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging
|
|
| 848 |
* to <i>this</i> taxon. The taxon relationship will also be removed from the set |
|
| 849 |
* of {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the child taxon.
|
|
| 850 |
* Furthermore the inherited RelatedFrom and RelatedTo attributes of the |
|
| 851 |
* taxon relationship will be nullified.<P> |
|
| 852 |
* Since the taxon relationship concerns the classification modifications |
|
| 853 |
* of the number of {@link #getTaxonomicChildrenCount() childrens} for <i>this</i> taxon and
|
|
| 854 |
* of the {@link #getTaxonomicParent() parent taxon} for the child taxon will be stored.
|
|
| 855 |
* |
|
| 856 |
* @param child the taxon playing the source role in the relationship to be removed |
|
| 857 |
* @see #removeTaxonRelation(TaxonRelationship) |
|
| 858 |
* @see #getRelationsToThisTaxon() |
|
| 859 |
* @see #getRelationsFromThisTaxon() |
|
| 860 |
* @see #getTaxonomicParent() |
|
| 861 |
* @see #getTaxonomicChildrenCount() |
|
| 862 |
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom() |
|
| 863 |
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedTo() |
|
| 864 |
* |
|
| 865 |
*/ |
|
| 866 |
@Deprecated //will be removed in future versions. Use classification/TaxonNode instead |
|
| 867 |
public void removeTaxonomicChild(Taxon child){
|
|
| 868 |
Set<TaxonRelationship> taxRels = this.getTaxonRelations(); |
|
| 869 |
for (TaxonRelationship taxRel : taxRels ){
|
|
| 870 |
if (taxRel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) |
|
| 871 |
&& taxRel.getFromTaxon().equals(child)){
|
|
| 872 |
this.removeTaxonRelation(taxRel); |
|
| 873 |
} |
|
| 874 |
} |
|
| 875 |
} |
|
| 876 |
|
|
| 877 |
/** |
|
| 878 |
* Returns the taxon which is the next higher taxon (parent) of <i>this</i> taxon |
|
| 879 |
* within the classification and which is stored in the |
|
| 880 |
* TaxonomicParentCache attribute. Each taxon can have only one parent taxon. |
|
| 881 |
* The child taxon and the parent taxon play the source respectively the |
|
| 882 |
* target role in one {@link TaxonRelationship taxon relationship} with
|
|
| 883 |
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
| 884 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 885 |
* than the rank of the taxon name used as a child taxon. |
|
| 886 |
* |
|
| 887 |
* @see #setTaxonomicParent(Taxon, Reference, String) |
|
| 888 |
* @see #getTaxonomicChildren() |
|
| 889 |
* @see #getTaxonomicChildrenCount() |
|
| 890 |
* @see #getRelationsFromThisTaxon() |
|
| 891 |
*/ |
|
| 892 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 893 |
public Taxon getTaxonomicParent() {
|
|
| 894 |
return this.taxonomicParentCache; |
|
| 895 |
} |
|
| 896 |
|
|
| 897 |
/** |
|
| 898 |
* Sets the taxononomic parent of <i>this</i> taxon to null. |
|
| 899 |
* Note that this method does not handle taxonomic relationships. |
|
| 900 |
*/ |
|
| 901 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 902 |
public void nullifyTaxonomicParent() {
|
|
| 903 |
this.taxonomicParentCache = null; |
|
| 904 |
} |
|
| 905 |
|
|
| 906 |
/** |
|
| 907 |
* Replaces both the taxonomic parent cache with the given new parent taxon |
|
| 908 |
* and the corresponding taxon relationship with a new {@link TaxonRelationship taxon relationship}
|
|
| 909 |
* (with {@link TaxonRelationshipType taxon relationship type} "taxonomically included in") instance.
|
|
| 910 |
* In the new taxon relationship <i>this</i> taxon plays the source role (child). |
|
| 911 |
* This method creates and adds the new taxon relationship to the set of |
|
| 912 |
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to <i>this</i> taxon.
|
|
| 913 |
* The taxon relationship will also be added to the set of |
|
| 914 |
* {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging to the second taxon
|
|
| 915 |
* (parent) involved in the new relationship.<P> |
|
| 916 |
* Since the taxon relationship concerns the classification modifications |
|
| 917 |
* of the {@link #getTaxonomicParent() parent taxon} for <i>this</i> taxon and of the number of
|
|
| 918 |
* {@link #getTaxonomicChildrenCount() childrens} for the child taxon will be stored.
|
|
| 919 |
* |
|
| 920 |
* @param newParent the taxon which plays the target role (parent) in the new taxon relationship |
|
| 921 |
* @param citation the reference source for the new taxon relationship |
|
| 922 |
* @param microcitation the string with the details describing the exact localisation within the reference |
|
| 923 |
* @see #removeTaxonRelation(TaxonRelationship) |
|
| 924 |
* @see #getTaxonomicParent() |
|
| 925 |
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String) |
|
| 926 |
* @see #addTaxonRelation(TaxonRelationship) |
|
| 927 |
* @see #getTaxonRelations() |
|
| 928 |
* @see #getRelationsFromThisTaxon() |
|
| 929 |
* @see #getRelationsToThisTaxon() |
|
| 930 |
* @see #getTaxonomicChildrenCount() |
|
| 931 |
*/ |
|
| 932 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 933 |
public void setTaxonomicParent(Taxon newParent, Reference citation, String microcitation){
|
|
| 934 |
//remove previously existing parent relationship!!! |
|
| 935 |
Taxon oldParent = this.getTaxonomicParent(); |
|
| 936 |
Set<TaxonRelationship> taxRels = this.getTaxonRelations(); |
|
| 937 |
for (TaxonRelationship taxRel : taxRels ){
|
|
| 938 |
if (taxRel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && taxRel.getToTaxon().equals(oldParent)){
|
|
| 939 |
this.removeTaxonRelation(taxRel); |
|
| 940 |
} |
|
| 941 |
} |
|
| 942 |
//add new parent |
|
| 943 |
if (newParent != null){
|
|
| 944 |
addTaxonRelation(newParent, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),citation,microcitation); |
|
| 945 |
} |
|
| 946 |
} |
|
| 947 |
|
|
| 948 |
/** |
|
| 949 |
* Returns the set of taxa which have <i>this</i> taxon as next higher taxon |
|
| 950 |
* (parent) within the classification. Each taxon can have several child |
|
| 951 |
* taxa. The child taxon and the parent taxon play the source respectively |
|
| 952 |
* the target role in one {@link TaxonRelationship taxon relationship} with
|
|
| 953 |
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
| 954 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 955 |
* than the rank of the taxon name used as a child taxon. |
|
| 956 |
* |
|
| 957 |
* @see #getTaxonomicParent() |
|
| 958 |
* @see #addTaxonomicChild(Taxon, Reference, String) |
|
| 959 |
* @see #getTaxonomicChildrenCount() |
|
| 960 |
* @see #getRelationsToThisTaxon() |
|
| 961 |
*/ |
|
| 962 |
@Transient |
|
| 963 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 964 |
public Set<Taxon> getTaxonomicChildren() {
|
|
| 965 |
Set<Taxon> taxa = new HashSet<Taxon>(); |
|
| 966 |
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon(); |
|
| 967 |
for (TaxonRelationship rel: rels){
|
|
| 968 |
TaxonRelationshipType tt = rel.getType(); |
|
| 969 |
TaxonRelationshipType incl = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); |
|
| 970 |
if (tt.equals(incl)){
|
|
| 971 |
taxa.add(rel.getFromTaxon()); |
|
| 972 |
} |
|
| 973 |
} |
|
| 974 |
return taxa; |
|
| 975 |
} |
|
| 976 |
|
|
| 977 |
/** |
|
| 978 |
* Returns the number of taxa which have <i>this</i> taxon as next higher taxon |
|
| 979 |
* (parent) within the classification and the number of which is stored in |
|
| 980 |
* the TaxonomicChildrenCount attribute. Each taxon can have several child |
|
| 981 |
* taxa. The child taxon and the parent taxon play the source respectively |
|
| 982 |
* the target role in one {@link TaxonRelationship taxon relationship} with
|
|
| 983 |
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
| 984 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 985 |
* than the rank of the taxon name used as a child taxon. |
|
| 986 |
* |
|
| 987 |
* @see #getTaxonomicChildren() |
|
| 988 |
* @see #getRelationsToThisTaxon() |
|
| 989 |
*/ |
|
| 990 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 991 |
public int getTaxonomicChildrenCount(){
|
|
| 992 |
return taxonomicChildrenCount; |
|
| 993 |
} |
|
| 994 |
|
|
| 995 |
/** |
|
| 996 |
* @see #getTaxonomicChildrenCount() |
|
| 997 |
*/ |
|
| 998 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 999 |
public void setTaxonomicChildrenCount(int taxonomicChildrenCount) {
|
|
| 1000 |
this.taxonomicChildrenCount = taxonomicChildrenCount; |
|
| 1001 |
} |
|
| 1002 |
|
|
| 1003 |
/** |
|
| 1004 |
* Returns the boolean value indicating whether <i>this</i> taxon has at least one |
|
| 1005 |
* taxonomic child taxon within the classification (true) or not (false). |
|
| 1006 |
* |
|
| 1007 |
* @see #getTaxonomicChildrenCount() |
|
| 1008 |
* @see #getTaxonomicChildren() |
|
| 1009 |
*/ |
|
| 1010 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 1011 |
@Transient |
|
| 1012 |
public boolean hasTaxonomicChildren(){
|
|
| 1013 |
return this.taxonomicChildrenCount > 0; |
|
| 1014 |
} |
|
| 1015 |
|
|
| 1016 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 1017 |
private int computeTaxonomicChildrenCount(){
|
|
| 1018 |
int count = 0; |
|
| 1019 |
for (TaxonRelationship rel: this.getRelationsToThisTaxon()){
|
|
| 1020 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
|
|
| 1021 |
count++; |
|
| 1022 |
} |
|
| 1023 |
} |
|
| 1024 |
return count; |
|
| 1025 |
} |
|
| 1026 |
|
|
| 1027 |
|
|
| 1028 | 784 |
/** |
| 1029 | 785 |
* Returns the boolean value indicating whether <i>this</i> taxon is a misaplication |
| 1030 | 786 |
* (misapplied name) for at least one other taxon. |
Also available in: Unified diff
ref #6089 Remove all calls and methods for taxonomicChildrenCount and taxonomicParentCache